1 Introduction

Pollen data can be used to do paleo-temperature reconstructions. However, this type of modeling can be affected by a lot of different aspects, such as paleoecological processes, chronology, and topographic effects on communities and species.

However, improvements in these techniques, and the increasing breadth of paleoclimatic proxies available have furthered our understanding of the effects of climate-driven variability on past societies.

This program allows you to reconstruct the climate for multiple locations across North America (when data are sufficient to do). In the program below, you can download fossil and modern data from the Neotoma Paleoecology Database, then compile the data using Williams and Shuman (2008) so that there will be columns of taxa with counts, as well as metadata attached to each of those records/rows. Some data in Neotoma overlaps with what was used by Whitmore et al. (2005) in the North American Modern Pollen Database, which can be obtained from one of two sources the Laboratory for Paleoclimatology and Climatology at the University of Ottawa and the Williams Paleoecology Lab at the University of Wisconsin. However, data from the North American Pollen Database is constantly being uploaded to Neotoma, and in some cases corrections are being made to the data too.

2 Load and cleanup modern data (i.e., pollen, climate, and locations)

2.1 Modern Pollen Data from Neotoma

2.2 Modern Pollen Data from “Core tops” of the Fossil Pollen Dataset in Neotoma

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## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
## API call was successful. Returned chronology.
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The Neotoma Modern Pollen Database contains 2597 samples, representing 100 different pollen taxa.

2.3 Map Modern Pollen Sample Locations

To examine locations of the modern pollen data, we can use leaflet to plot the modern pollen locations.

3 Load Prism Climate Data

The first step is to get the locations of the Modern Pollen samples. Next, we use a PRISM climate extraction script, which is adapted from Bocinsky et al. (2016).

## OGR data source with driver: ESRI Shapefile 
## Source: "/Volumes/VILLAGE/SKOPEII/MAT/WORKING/paleomat/data/statesp010g.shp_nt00938", layer: "statesp010g"
## with 61 features
## It has 11 fields

4 Load WorldClim Climate Data

WorldClim 2.0 has 31 years (1970-2000) of averaged climate data and here we use a resolution of 30 seconds (~1 km2).

4.1 Clean up datasets to remove NAs

Need to further clean up the datasets to remove any rows with NA values. Although currently working with United States data, we do not currently have climate (prism) data for Alaska, which is the reason for all rows with NAs.

Modern Pollen data contains 1416 samples, representing 100 different pollen taxa.

4.1.1 Checking the calibration data set

To test the model, I used the palaeoSig package’s randomTF() function, which tests the models against randomly sorted data. If we do get a significance for a climate variable, then we know that the model reconstruction is better than random. The model takes the proportion of variance accounted for by the actual data, and then compares it to the proportion of variance accounted for by the randomized data. Here, we use a wrapper function for randomTF.

The MAT method is testing whether the modern calibration is able to detect signals in each of the climate parameters. The example here uses the entire North American Modern Pollen Database, rather than a targeted data subset.

4.1.1.1 WA - Monotone Deshrinking

% Explained p-value
tjan 0.13 0.06
tfeb 0.12 0.07
tmar 0.13 0.05
tapr 0.13 0.04
tmay 0.14 0.04
tjun 0.14 0.04
tjul 0.14 0.04
taug 0.14 0.04
tsep 0.14 0.04
toct 0.14 0.04
tnov 0.14 0.04
tdec 0.13 0.05

The columns are standard weighted average. One positive of using monotone shrinking is that it does not suffer from spatial-autocorrelation like with using MAT. Therefore, there has been quite a bit of criticism against MAT. You can do a spatial variogram of the model, then test to see if it is significant. MAT gives you a root mean error that is much higher than what it probably really is. Sometimes it is just because the cores are so close to one another, more so than the assemblages reflect climate. Consider weighted averaging (partially squared not really worth it. ) Weighted averaging with the monotone shrinking is very fast.

4.1.1.2 MAT - ten closest

% Explained p-value
tjan 0.06 0.01
tfeb 0.06 0.01
tmar 0.06 0.01
tapr 0.07 0.01
tmay 0.07 0.01
tjun 0.08 0.01
tjul 0.08 0.01
taug 0.08 0.01
tsep 0.07 0.01
toct 0.07 0.01
tnov 0.06 0.01
tdec 0.06 0.01

The variance explained is very low for some variables, although the p value is very low. This highlights that in some cases you may not just want to rely on the p value. This also shows the issue with temporal autocorrelation on temperature and, to some extent also, on precipitation variables.

5 Reconstruction Statistics

5.1 Reconstruction Significance

Now we can do a similar test on fossil assemblage reconstructions. This again uses the same randomTF() function, but the variance explained and significance will probably change given that we are using a slightly more constrained dataset.

5.1.1 Obtaining a fossil pollen record from Neotoma

Now, we apply a reconstruction to a real dataset. The record has coverage across multiple timescales. For this example, we will restrict the analysis to a record from Colorado.

# Use gpids to get the Four Corners area (or geopolitical unit) in North America.
# Then get the datasets for the pollen data from each of the gpids.

# Retrieve the GeoPolitical Units table, which has country, state, and county level names 
# with associated IDs. 
gpids <- get_table(table.name='GeoPoliticalUnits')

# Currently using a work around to get data from specific sites by defining the states in 
# the Neotoma GeoPolitical Units table (http://api.neotomadb.org/apdx/geopol.htm). It 
# occasionally will not pull in the correct data. This is the same thing that was done 
# with the modern pollen data from Neotoma above.
SWID <-  gpids %>%
  dplyr::filter(GeoPoliticalName %in% c('Colorado', 'Utah', 'Arizona', 'New Mexico', 'Texas'),
              GeoPoliticalUnit == 'state') %$%
  GeoPoliticalID

# We want to restrict to fossil pollen datasets for the Four Corners from the last 
# 2000 years.
UUSS_sites <- neotoma::get_dataset(ageold = 2000, 
                                  ageyoung = -50, 
                                  gpid = SWID,
                                  datasettype = 'pollen')

# Here, we map the dataset IDs to the FourCorners, so that we can use this for mapping 
# below.
datasets <- UUSS_sites %>% map_int(function(x) x$dataset.meta$dataset.id)

This returns 59 sites. The neotoma package provides plotting capabilities, but leaflet allows for more interactive plotting.

Data record 12 within the Upper United States Southwest data represents Eldora Fen, Colorado, recorded by Louis J.Maher Jr. The record spans 7,900 years, which provides some information for environmental change at the site.

# Another step from Neotoma, we need to download the data for the site.
EldoraFen <- get_download(UUSS_sites[[12]])
## API call was successful. Returned record for Eldora Fen
# Here we can also use Stratiplot to look at the pollen profile and change over time for 
# the Eldora Fen site.
analogue::Stratiplot(EldoraFen$`790`$sample.meta$age ~ 
                       Juniperus + 
                       `Pinus undiff.` + 
                       Salix + 
                       Quercus,
                   data = (as.data.frame(EldoraFen$`790`$counts)), 
                   xlab = "Counts", 
                   ylab = "Age")

Using the complete North American dataset, we focus on a reconstruction of summer temperature for this record (tjul). We also need to clean up the data sets too:

5.1.1.1 WA - Monotone Deshrinking

% Explained p-value
tjan 0.21 0.70
tfeb 0.20 0.80
tmar 0.24 0.61
tapr 0.27 0.52
tmay 0.29 0.50
tjun 0.29 0.49
tjul 0.26 0.53
taug 0.28 0.50
tsep 0.31 0.44
toct 0.34 0.41
tnov 0.31 0.46
tdec 0.24 0.61

5.1.1.2 MAT - ten closest

% Explained p-value
tjan 0.20 0.25
tfeb 0.20 0.25
tmar 0.13 0.43
tapr 0.11 0.49
tmay 0.26 0.15
tjun 0.23 0.19
tjul 0.20 0.25
taug 0.20 0.26
tsep 0.24 0.17
toct 0.23 0.19
tnov 0.12 0.46
tdec 0.18 0.32

Again, no significance for the model. This indicates that we are just not able to see a signal within the data, but this is probably due to the calibration dataset being too broad.

5.2 Reconstruction

Once we have validated the methods, we re-run the analyses using the two methods, MAT and WA.

5.2.1 Model Summary

6 Saving to file

Save values to file.